LAMMPS (17 Feb 2022)
#===========================================================================#
#  System of colloidal particles under shear.                               #
#                                                                           #
#  Run consists of 10x12x4 particles, each composed of 3613 particle nodes  #
#    (3612 particles forming a spherical shell, and 1 central particle).    #
#  280 x 280 x 101 lattice-Boltzmann grid sites.                            #
#                                                                           #
#  This simulation is used to illustrate the simulation time of a realistic #
#    implementation of the lb/fluid fix.                                    #
#  The data file "confinedcolloids.dat" is quite large and so is not        #
#  included here.  It can be obtained from:                                 #
#  http://publish.uwo.ca/~cdennist/confinedcolloids.dat.gz                  #
#                                                                           #
#  Sample output from this run can be found in the file:                    #
#    results64.out                                                          #
#===========================================================================#

units       micro
dimension   3
boundary    p p f
atom_style  molecular
read_data   confinedcolloids.dat
Reading data file ...
  orthogonal box = (0 0 0) to (16.8 16.8 6)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  1734240 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.372 seconds
  read_data CPU = 34.950 seconds

mass * 0.00010287

#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
#   to ensure that the particles belonging to a given processor remain inside
#   that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
#   to ensure that the particles belonging to a given processor remain inside
#   that processors lattice-Boltzmann grid.  However, these values can likely
#   be somewhat increased without issue.  If a problem does arise (a particle
#   is outside of its processors LB grid) an error message is printed and
#   the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.03 bin
neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1

#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each colloidal object which
#   do not interact with the fluid, but are used to implement the hard-sphere
#   interactions.
#----------------------------------------------------------------------------
group ForceAtoms type 1
480 atoms in group ForceAtoms

#----------------------------------------------------------------------------
# FluidAtoms are the particles representing the surface of the colloidal
#   object which do interact with the fluid.
#----------------------------------------------------------------------------
group FluidAtoms type 2
1733760 atoms in group FluidAtoms

#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
#   each colloidal object (use a truncated and shifted Lennard-Jones
#   potential).
#----------------------------------------------------------------------------
pair_style lj/cut 1.572
pair_coeff * * 0.0 0.0 1.572
pair_coeff 1 1 10.0 1.400492785 1.572
pair_modify shift yes

timestep 0.001

#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
#   (however, this fix does not explicitly apply a force back on to these
#    particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid density = 1.0, fluid viscosity = 1.0, (water at STP) and a
# lattice spacing dx=0.06.
# Implement top/bottomw walls moving at speeds of 20.0 in opposite directions
#----------------------------------------------------------------------------
fix   1 FluidAtoms lb/fluid 1 1.0 1.0 dx 0.06 zwall_velocity -20.0 20.0
Using a lattice-Boltzmann grid of 280 by 280 by 101 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)

#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
#   these atoms represent the surface of the colloidal object, which should
#   interact with the fluid).
#----------------------------------------------------------------------------
fix   2 FluidAtoms lb/viscous

#----------------------------------------------------------------------------
# Each colloidal object (spherical shell of particles and central particle)
#   is specified as a separate molecule in the confinedcolloids.dat data
#   file.  Integrate the motion of each of these sets of particles as rigid
#   objects which move and rotate together.
#----------------------------------------------------------------------------
fix   3 all rigid molecule
  480 rigid bodies with 1734240 atoms

#----------------------------------------------------------------------------
# Implement a repulsive interaction between the ForceAtoms particles, and the
#   upper and lower z-walls. (A truncated and shifted Lennard-Jones potential
#   is used).
#----------------------------------------------------------------------------
fix   wallhi ForceAtoms wall/lj126 zhi 5.88 20.0 0.8071542386 0.906 units box
fix   walllo ForceAtoms wall/lj126 zlo 0.0  20.0 0.8071542386 0.906 units box

#dump  ParticleTracking ForceAtoms custom 50 test.track id mol x y z vx vy vz

thermo 50

#run   400
run 100

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix lb/fluid command:

@Article{Denniston et al.,
 author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
 title =   {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
 year =    2022,
 volume =  275,
 pages =   {108318}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.602
  ghost atom cutoff = 1.602
  binsize = 0.801, bins = 21 21 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 373.3 | 373.3 | 373.3 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0            0            0            0            0 
      50    4511970.8            0            0    89.610701   0.21526205 
     100     16113793            0            0     320.0305  -0.54714356 
Loop time of 2168.87 on 4 procs for 100 steps with 1734240 atoms

Performance: 3983.646 ns/day, 0.006 hours/ns, 0.046 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.67377    | 0.70143    | 0.72779    |   2.5 |  0.03
Bond    | 4.19e-05   | 6.0825e-05 | 7.85e-05   |   0.0 |  0.00
Neigh   | 1978.7     | 1982.4     | 1985.9     |   6.3 | 91.40
Comm    | 9.4132     | 12.886     | 16.538     |  78.3 |  0.59
Output  | 0.0089264  | 0.016853   | 0.024638   |   4.3 |  0.00
Modify  | 171.19     | 171.23     | 171.27     |   0.3 |  7.89
Other   |            | 1.598      |            |       |  0.07

Nlocal:         433560 ave      433560 max      433560 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:         397888 ave      397888 max      397888 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:             60 ave          60 max          60 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 240
Ave neighs/atom = 0.00013838915
Ave special neighs/atom = 0
Neighbor list builds = 16
Dangerous builds = 0
Total wall time: 0:39:00
